Is CCDC47 p.Asp255Gly (c.764A>G) pathogenic?

CCDC47 p.Asp255Gly (c.764A>G) is classified Uncertain significance in CCDC47 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-04). AlphaMissense: likely pathogenic (0.7145); Very rare (popmax 0.0017%, nfe).

How common is CCDC47 p.Asp255Gly (c.764A>G) in the general population?

CCDC47 p.Asp255Gly (c.764A>G) is very rare (popmax 0.0017%, nfe) (gnomAD).

What do computational predictors say about CCDC47 p.Asp255Gly (c.764A>G)?

AlphaMissense predicts likely pathogenic (score 0.7145) — an in-silico prediction, not a clinical call.

CCDC47 p.Asp255Gly

c.764A>G · rs776982310 · VCV2395691

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7145 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0017%, nfe)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.7145	likely pathogenic
REVEL	0.365	indeterminate
SaProt	LLR -13.73	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.8	GERP 5.2, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 19 kb · p 0.0049 · regional, not allelic
Overall
CADD	28.2	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0017% European (non-Finnish) · 20/1,179,490 alleles

Filtering AF 0.00111% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0009%

Overall 0.00144% 21/1,461,254 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0017%	58,974
Remaining individualsnot grpmax-eligible	0.0016%	62,496

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CCDC47
Protein: p.Asp255Gly
Coding: c.764A>G
MANE Select: NM_020198
dbSNP: rs776982310
Type: single nucleotide variant
Location: chr17:63756542 (GRCh38)
Gene constraint: LOEUF 0.918 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.07 · 1 PDB

Full CCDC47 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC47 p.Arg397Ter Pathogenic/Likely pathogenic ★★ same type
CCDC47 p.Asp75Tyr Uncertain significance ★★ ⚠ same type
CCDC47 p.Trp133Arg Uncertain significance ★★ ⚠ same type
CCDC47 c.1093+112G>A Benign ★★ same type
CCDC47 c.1094-3C>T Benign ★★ same type
CCDC47 c.735+15C>T Benign ★★ same type
CCDC47 p.Arg271Ter Likely pathogenic ★ same type
CCDC47 c.669+5G>T Uncertain significance ★ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ccdc47-p-asp255gly (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown